WO2002046363A3 - Improved methods for gene expression monitoring on electronic microarrays - Google Patents

Improved methods for gene expression monitoring on electronic microarrays Download PDF

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Publication number
WO2002046363A3
WO2002046363A3 PCT/US2001/046128 US0146128W WO0246363A3 WO 2002046363 A3 WO2002046363 A3 WO 2002046363A3 US 0146128 W US0146128 W US 0146128W WO 0246363 A3 WO0246363 A3 WO 0246363A3
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WIPO (PCT)
Prior art keywords
gene expression
methods
hybridization
sample
amplicons
Prior art date
Application number
PCT/US2001/046128
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French (fr)
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WO2002046363A2 (en
Inventor
Elaine M Weidenhammer
Ling Wang
Xiao Xu
Michael J Heller
Brenda F Kahl
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Nanogen Inc
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Publication date
Application filed by Nanogen Inc filed Critical Nanogen Inc
Priority to EP01988251A priority Critical patent/EP1341932A4/en
Priority to JP2002548082A priority patent/JP2004524823A/en
Priority to AU2002241574A priority patent/AU2002241574A1/en
Publication of WO2002046363A2 publication Critical patent/WO2002046363A2/en
Publication of WO2002046363A3 publication Critical patent/WO2002046363A3/en

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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
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    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
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    • B82—NANOTECHNOLOGY
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    • C07—ORGANIC CHEMISTRY
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    • C07K1/045—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers using devices to improve synthesis, e.g. reactors, special vessels
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
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    • G11C13/0014—RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material
    • G11C13/0019—RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material comprising bio-molecules
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    • G11—INFORMATION STORAGE
    • G11C—STATIC STORES
    • G11C19/00—Digital stores in which the information is moved stepwise, e.g. shift registers
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    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
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    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00306—Reactor vessels in a multiple arrangement
    • B01J2219/00313—Reactor vessels in a multiple arrangement the reactor vessels being formed by arrays of wells in blocks
    • B01J2219/00315—Microtiter plates
    • B01J2219/00317—Microwell devices, i.e. having large numbers of wells
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Abstract

The present invention presents methods for gene expression monitoring that utilize microelectronic arrays to drive the transport and hybridization of nucleic acids. Procedures are described for generating mRNA expression samples for use in these methods from populations of cells, tissues, or other biological source materials, that may differ in their physiological and/or pathological state. Provided in the invention are methods for generating a reusable nucleic acid transcript library from mRNA in a sample of biological material. In order to improve gene expression monitoring on the microelectronic arrays, the transcripts are amplified to produce sample nucleic acid amplicons of a defined length. Because multiple sample amplicons may be selectively hybridized to controlled sites in the electronic array, the gene expression profiles of the polynucleotide populations from different sources can be directly compared in an array format using electronic hybridization methodologies. Also provided in the invention are methods for detecting the level of sample amplicons using electronically assisted primer extension detection, and utilizing individual test site hybridization controls. The hybridization data collected utilizing the improved methods of the present invention will allow the correlation of changes in mRNA level with the corresponding expression of the encoded protein in the biological source material, and thus aid in studying the role of gene expression in disease.
PCT/US2001/046128 2000-11-09 2001-10-30 Improved methods for gene expression monitoring on electronic microarrays WO2002046363A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP01988251A EP1341932A4 (en) 2000-11-09 2001-10-30 Improved methods for gene expression monitoring on electronic microarrays
JP2002548082A JP2004524823A (en) 2000-11-09 2001-10-30 An improved method for monitoring gene expression on electrical microarrays
AU2002241574A AU2002241574A1 (en) 2000-11-09 2001-10-30 Improved methods for gene expression monitoring on electronic microarrays

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US09/710,200 US6379897B1 (en) 2000-11-09 2000-11-09 Methods for gene expression monitoring on electronic microarrays
US09/710,200 2000-11-09

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WO2002046363A2 WO2002046363A2 (en) 2002-06-13
WO2002046363A3 true WO2002046363A3 (en) 2002-08-15

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US (3) US6379897B1 (en)
EP (1) EP1341932A4 (en)
JP (1) JP2004524823A (en)
WO (1) WO2002046363A2 (en)

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EP1341932A4 (en) 2005-11-23
US20020119484A1 (en) 2002-08-29
US6379897B1 (en) 2002-04-30
JP2004524823A (en) 2004-08-19
US20020150917A1 (en) 2002-10-17
US6492122B2 (en) 2002-12-10
WO2002046363A2 (en) 2002-06-13
EP1341932A2 (en) 2003-09-10

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